diff --git a/internal/pkg/clean.go b/internal/pkg/clean.go
new file mode 100644
index 00000000..addcd32d
--- /dev/null
+++ b/internal/pkg/clean.go
@@ -0,0 +1,138 @@
+package pkg
+
+import (
+	"errors"
+	"os"
+	"unique"
+)
+
+// Clean destroys checksum backing entries without any identifier or substitute
+// entry referring to it. If at least one keep [Artifact] is specified,
+// identifier and substitute entries not kept alive by them are destroyed first.
+func (c *Cache) Clean(dry, inputs bool, keep ...Artifact) (
+	[]unique.Handle[ID],
+	[]unique.Handle[Checksum],
+	error,
+) {
+	c.identMu.Lock()
+	defer c.identMu.Unlock()
+
+	c.checksumMu.Lock()
+	defer c.checksumMu.Unlock()
+
+	dents, err := os.ReadDir(c.base.Append(dirChecksum).String())
+	if err != nil {
+		return nil, nil, err
+	}
+	checksums := make(map[unique.Handle[Checksum]]string, len(dents))
+	var buf Checksum
+	for _, dent := range dents {
+		name := dent.Name()
+		if err = Decode(&buf, name); err != nil {
+			return nil, nil, err
+		}
+		checksums[unique.Make(buf)] = name
+	}
+
+	type identPair struct {
+		id   unique.Handle[ID]
+		name string
+	}
+	dents, err = os.ReadDir(c.base.Append(dirIdentifier).String())
+	if err != nil {
+		return nil, nil, err
+	}
+
+	keepIdents := make(map[unique.Handle[ID]]struct{})
+	if inputs {
+		for _, id := range Inputs((*Collect)(&keep)) {
+			keepIdents[id] = struct{}{}
+		}
+	} else {
+		for _, a := range keep {
+			keepIdents[c.Ident(a)] = struct{}{}
+		}
+	}
+
+	idents := make([]identPair, 0, len(dents))
+	for _, dent := range dents {
+		name := dent.Name()
+		if err = Decode(&buf, name); err != nil {
+			return nil, nil, err
+		}
+		id := unique.Make(ID(buf))
+
+		if _, ok := keepIdents[id]; len(keep) == 0 || ok {
+			if err = readlinkChecksum(c.base.Append(
+				dirIdentifier,
+				name,
+			), &buf); err != nil {
+				return nil, nil, err
+			}
+			delete(checksums, unique.Make(buf))
+			continue
+		}
+
+		c.msg.Verbosef("arranging for destruction of %s...", name)
+		idents = append(idents, identPair{id, name})
+	}
+
+	destroyedIdents := make([]unique.Handle[ID], 0, len(idents))
+	for _, pair := range idents {
+		if !dry {
+			if err = os.Remove(c.base.Append(
+				dirIdentifier,
+				pair.name,
+			).String()); err != nil {
+				return destroyedIdents, nil, err
+			}
+		}
+		destroyedIdents = append(destroyedIdents, pair.id)
+	}
+
+	destroyedChecksums := make([]unique.Handle[Checksum], 0, len(checksums))
+	for checksum, name := range checksums {
+		if err = c.parent.Err(); err != nil {
+			return destroyedIdents, destroyedChecksums, err
+		}
+		c.msg.Verbosef("destroying checksum %s...", name)
+		if !dry {
+			if err = errors.Join(removeAll(c.base.Append(
+				dirChecksum,
+				name,
+			))); err != nil {
+				return destroyedIdents, destroyedChecksums, err
+			}
+		}
+		destroyedChecksums = append(destroyedChecksums, checksum)
+	}
+
+	dents, err = os.ReadDir(c.base.Append(dirSubstitute).String())
+	if err != nil {
+		return destroyedIdents, destroyedChecksums, err
+	}
+	for _, dent := range dents {
+		name := dent.Name()
+		if err = readlinkChecksum(c.base.Append(
+			dirSubstitute,
+			name,
+		), &buf); err != nil {
+			return destroyedIdents, destroyedChecksums, err
+		}
+		if _, ok := checksums[unique.Make(buf)]; !ok {
+			continue
+		}
+
+		c.msg.Verbosef("destroying substitute %s...", name)
+		if !dry {
+			if err = os.Remove(c.base.Append(
+				dirSubstitute,
+				name,
+			).String()); err != nil {
+				return destroyedIdents, destroyedChecksums, err
+			}
+		}
+	}
+
+	return destroyedIdents, destroyedChecksums, nil
+}
diff --git a/internal/pkg/clean_test.go b/internal/pkg/clean_test.go
new file mode 100644
index 00000000..1b93185c
--- /dev/null
+++ b/internal/pkg/clean_test.go
@@ -0,0 +1,312 @@
+package pkg_test
+
+import (
+	"bytes"
+	"crypto/sha512"
+	"io/fs"
+	"log"
+	"os"
+	"path/filepath"
+	"slices"
+	"strings"
+	"testing"
+	"unique"
+
+	"hakurei.app/check"
+	"hakurei.app/internal/pkg"
+	"hakurei.app/message"
+)
+
+// formatHandles returns a user-facing string representing h.
+func formatHandles[T pkg.ID | pkg.Checksum](handles ...unique.Handle[T]) string {
+	var buf strings.Builder
+	for _, h := range handles {
+		buf.WriteString(pkg.Encode(pkg.Checksum(h.Value())))
+		buf.WriteString(", ")
+	}
+	return strings.TrimSuffix(buf.String(), ", ")
+}
+
+func TestClean(t *testing.T) {
+	t.Parallel()
+	ic := pkg.NewIR()
+
+	testCases := []struct {
+		name   string
+		a      []pkg.Artifact
+		keep   []pkg.Artifact
+		inputs bool
+		want   expectsFS
+
+		wantIdents    []unique.Handle[pkg.ID]
+		wantChecksums []unique.Handle[pkg.Checksum]
+	}{
+		{"simple", []pkg.Artifact{
+			pkg.NewFile("file", nil),
+		}, nil, false, expectsFS{
+			".": {Mode: fs.ModeDir | 0700},
+
+			"checksum": {Mode: fs.ModeDir | 0700},
+			"checksum/OLBgp1GsljhM2TJ-sbHjaiH9txEUvgdDTAzHv2P24donTt6_529l-9Ua0vFImLlb": {Mode: 0400},
+
+			"identifier": {Mode: fs.ModeDir | 0700},
+			"identifier/pPRjw2XYgjB5k8dYedwxTBMgHh4_v2JM_G2Vd-skQbAGOOgPsl3CGSUbEF7om_MO": {Mode: fs.ModeSymlink | 0777, Data: []byte("../checksum/OLBgp1GsljhM2TJ-sbHjaiH9txEUvgdDTAzHv2P24donTt6_529l-9Ua0vFImLlb")},
+
+			"lock":       {Mode: 0644},
+			"variant":    {Mode: 0400},
+			"status":     {Mode: fs.ModeDir | 0700},
+			"substitute": {Mode: fs.ModeDir | 0700},
+			"fault":      {Mode: fs.ModeDir | 0700},
+			"work":       {Mode: fs.ModeDir | 0700},
+		}, nil, nil},
+
+		{"keep", []pkg.Artifact{
+			pkg.NewFile("removed-file", []byte("removed file")),
+		}, []pkg.Artifact{
+			pkg.NewFile("file", []byte("\xfd")),
+		}, false, expectsFS{
+			".": {Mode: fs.ModeDir | 0700},
+
+			"checksum": {Mode: fs.ModeDir | 0700},
+			"checksum/KgZ-FjbGuU-XP2QEHInpgv-2Zn0cTH5NqFMgTU0XrSdKmSwyC-3baVs1BMCP5spk": {Mode: 0400, Data: []byte("\xfd")},
+
+			"identifier": {Mode: fs.ModeDir | 0700},
+			"identifier/FMwSBYw22KqM8jZryfY2ChHXpLuVDdWYyNOYdHvIVYk8ujY6UnGRm5brr2sTTfpD": {Mode: fs.ModeSymlink | 0777, Data: []byte("../checksum/KgZ-FjbGuU-XP2QEHInpgv-2Zn0cTH5NqFMgTU0XrSdKmSwyC-3baVs1BMCP5spk")},
+
+			"lock":       {Mode: 0644},
+			"variant":    {Mode: 0400},
+			"status":     {Mode: fs.ModeDir | 0700},
+			"substitute": {Mode: fs.ModeDir | 0700},
+			"fault":      {Mode: fs.ModeDir | 0700},
+			"work":       {Mode: fs.ModeDir | 0700},
+		}, []unique.Handle[pkg.ID]{
+			ic.Ident(pkg.NewFile("removed-file", []byte("removed file"))),
+		}, []unique.Handle[pkg.Checksum]{
+			unique.Make(sha512.Sum384([]byte("removed file"))),
+		}},
+
+		{"inputs anchored substitute", []pkg.Artifact{
+			&stubArtifactF{
+				kind:   pkg.KindExec,
+				params: []byte("destroyed"),
+				deps: []pkg.Artifact{
+					pkg.NewFile("destroyed-input", []byte("destroyed")),
+				},
+				cure: func(f *pkg.FContext) error {
+					p := f.GetWorkDir()
+					if err := os.MkdirAll(p.String(), 0755); err != nil {
+						return err
+					}
+					return os.WriteFile(p.Append("result").String(), nil, 0444)
+				},
+			},
+		}, []pkg.Artifact{
+			&stubArtifactF{
+				kind:   pkg.KindExec,
+				params: []byte("kept"),
+				deps: []pkg.Artifact{
+					pkg.NewFile("kept-input", []byte("kept")),
+				},
+				cure: func(f *pkg.FContext) error {
+					p := f.GetWorkDir()
+					if err := os.MkdirAll(p.String(), 0755); err != nil {
+						return err
+					}
+					return os.WriteFile(p.Append("result").String(), nil, 0444)
+				},
+			},
+		}, true, expectsFS{
+			".": {Mode: fs.ModeDir | 0700},
+
+			"checksum": {Mode: fs.ModeDir | 0700},
+			"checksum/H-eSiCo227-xdqyNl2R-5G3eqXPtbb8XegAB70I5OQb2majeZXJoCxTq9wJy5qqv":        {Mode: 0400, Data: []byte("kept")},
+			"checksum/UjZSrgz7_B7XMd9fHU7jM33UZhWlFgX0rz7JZbCBYR28bCS7jr_CAJdcDhi52ruE":        {Mode: fs.ModeDir | 0500},
+			"checksum/UjZSrgz7_B7XMd9fHU7jM33UZhWlFgX0rz7JZbCBYR28bCS7jr_CAJdcDhi52ruE/result": {Mode: 0444},
+
+			"identifier": {Mode: fs.ModeDir | 0700},
+			"identifier/Ef8KX6s_rS_nLgze0rj90zKyrGAvOnzyU0DL7nrYQWEG_f4a9pmUKI6HBEMD8AE8": {Mode: fs.ModeSymlink | 0777, Data: []byte("../checksum/H-eSiCo227-xdqyNl2R-5G3eqXPtbb8XegAB70I5OQb2majeZXJoCxTq9wJy5qqv")},
+			"identifier/xoIGLemzLF227e-w_AJcf_1Sgqh2gs3KFgqvOIWUQE-9P_y2vHBMBytL4GRGQqTb": {Mode: fs.ModeSymlink | 0777, Data: []byte("../checksum/UjZSrgz7_B7XMd9fHU7jM33UZhWlFgX0rz7JZbCBYR28bCS7jr_CAJdcDhi52ruE")},
+
+			"lock":    {Mode: 0644},
+			"variant": {Mode: 0400},
+			"status":  {Mode: fs.ModeDir | 0700},
+
+			"substitute": {Mode: fs.ModeDir | 0700},
+			"substitute/4bjS-QjGcSV4nth-W6Vg3-wolKmKgiq4Ld2oRIWcOfy6Wi41XXLAWPoo8FcDx6BH": {Mode: fs.ModeSymlink | 0777, Data: []byte("../checksum/UjZSrgz7_B7XMd9fHU7jM33UZhWlFgX0rz7JZbCBYR28bCS7jr_CAJdcDhi52ruE")},
+			"substitute/dzO8FEY9lu4hwRT6BfRZOX-uYGsC_5XH4jEJ7sJyThcmG9J_w1ArOAaUCGfL8wAM": {Mode: fs.ModeSymlink | 0777, Data: []byte("../checksum/UjZSrgz7_B7XMd9fHU7jM33UZhWlFgX0rz7JZbCBYR28bCS7jr_CAJdcDhi52ruE")},
+
+			"fault": {Mode: fs.ModeDir | 0700},
+			"work":  {Mode: fs.ModeDir | 0700},
+		}, []unique.Handle[pkg.ID]{
+			ic.Ident(pkg.NewFile("destroyed-input", []byte("destroyed"))),
+			ic.Ident(&stubArtifactF{
+				kind:   pkg.KindExec,
+				params: []byte("destroyed"),
+				deps: []pkg.Artifact{
+					pkg.NewFile("destroyed-input", []byte("destroyed")),
+				},
+				cure: func(f *pkg.FContext) error {
+					p := f.GetWorkDir()
+					if err := os.MkdirAll(p.String(), 0755); err != nil {
+						return err
+					}
+					return os.WriteFile(p.Append("result").String(), nil, 0444)
+				},
+			}),
+		}, []unique.Handle[pkg.Checksum]{
+			unique.Make(sha512.Sum384([]byte("destroyed"))),
+		}},
+
+		{"inputs", []pkg.Artifact{
+			&stubArtifactF{
+				kind:   pkg.KindExec,
+				params: []byte("destroyed"),
+				deps: []pkg.Artifact{
+					pkg.NewFile("destroyed-input", []byte("destroyed")),
+				},
+				cure: func(f *pkg.FContext) error {
+					p := f.GetWorkDir()
+					if err := os.MkdirAll(p.String(), 0755); err != nil {
+						return err
+					}
+					return os.WriteFile(p.Append("result").String(), nil, 0444)
+				},
+			},
+		}, []pkg.Artifact{
+			&stubArtifactF{
+				kind:   pkg.KindExec,
+				params: []byte("kept"),
+				deps: []pkg.Artifact{
+					pkg.NewFile("kept-input", []byte("kept")),
+				},
+				cure: func(f *pkg.FContext) error {
+					p := f.GetWorkDir()
+					if err := os.MkdirAll(p.String(), 0755); err != nil {
+						return err
+					}
+					return os.WriteFile(p.Append("result").String(), []byte{0}, 0444)
+				},
+			},
+		}, true, expectsFS{
+			".": {Mode: fs.ModeDir | 0700},
+
+			"checksum": {Mode: fs.ModeDir | 0700},
+			"checksum/CyDnDvF-LaeGPcSW70tPosNCoclByWkTjznUUF1DcgzlIwkN9yzz1ZFME1TlPj6W":        {Mode: fs.ModeDir | 0500},
+			"checksum/CyDnDvF-LaeGPcSW70tPosNCoclByWkTjznUUF1DcgzlIwkN9yzz1ZFME1TlPj6W/result": {Mode: 0444, Data: []byte("\x00")},
+			"checksum/H-eSiCo227-xdqyNl2R-5G3eqXPtbb8XegAB70I5OQb2majeZXJoCxTq9wJy5qqv":        {Mode: 0400, Data: []byte("kept")},
+
+			"identifier": {Mode: fs.ModeDir | 0700},
+			"identifier/Ef8KX6s_rS_nLgze0rj90zKyrGAvOnzyU0DL7nrYQWEG_f4a9pmUKI6HBEMD8AE8": {Mode: fs.ModeSymlink | 0777, Data: []byte("../checksum/H-eSiCo227-xdqyNl2R-5G3eqXPtbb8XegAB70I5OQb2majeZXJoCxTq9wJy5qqv")},
+			"identifier/xoIGLemzLF227e-w_AJcf_1Sgqh2gs3KFgqvOIWUQE-9P_y2vHBMBytL4GRGQqTb": {Mode: fs.ModeSymlink | 0777, Data: []byte("../checksum/CyDnDvF-LaeGPcSW70tPosNCoclByWkTjznUUF1DcgzlIwkN9yzz1ZFME1TlPj6W")},
+
+			"lock":    {Mode: 0644},
+			"variant": {Mode: 0400},
+			"status":  {Mode: fs.ModeDir | 0700},
+
+			"substitute": {Mode: fs.ModeDir | 0700},
+			"substitute/4bjS-QjGcSV4nth-W6Vg3-wolKmKgiq4Ld2oRIWcOfy6Wi41XXLAWPoo8FcDx6BH": {Mode: fs.ModeSymlink | 0777, Data: []byte("../checksum/CyDnDvF-LaeGPcSW70tPosNCoclByWkTjznUUF1DcgzlIwkN9yzz1ZFME1TlPj6W")},
+
+			"fault": {Mode: fs.ModeDir | 0700},
+			"work":  {Mode: fs.ModeDir | 0700},
+		}, []unique.Handle[pkg.ID]{
+			ic.Ident(pkg.NewFile("destroyed-input", []byte("destroyed"))),
+			ic.Ident(&stubArtifactF{
+				kind:   pkg.KindExec,
+				params: []byte("destroyed"),
+				deps: []pkg.Artifact{
+					pkg.NewFile("destroyed-input", []byte("destroyed")),
+				},
+				cure: func(f *pkg.FContext) error {
+					p := f.GetWorkDir()
+					if err := os.MkdirAll(p.String(), 0755); err != nil {
+						return err
+					}
+					return os.WriteFile(p.Append("result").String(), nil, 0444)
+				},
+			}),
+		}, []unique.Handle[pkg.Checksum]{
+			unique.Make(expectsFS{
+				".":      {Mode: fs.ModeDir | 0500},
+				"result": {Mode: 0444},
+			}.hash()),
+			unique.Make(sha512.Sum384([]byte("destroyed"))),
+		}},
+	}
+	for _, tc := range testCases {
+		t.Run(tc.name, func(t *testing.T) {
+			t.Parallel()
+
+			base := check.MustAbs(t.TempDir())
+			if err := os.Chmod(base.String(), 0700); err != nil {
+				t.Fatal(err)
+			}
+			t.Cleanup(func() {
+				if err := filepath.WalkDir(base.String(), func(path string, d fs.DirEntry, err error) error {
+					if err != nil {
+						t.Error(err)
+						return nil
+					}
+					if !d.IsDir() {
+						return nil
+					}
+					return os.Chmod(path, 0700)
+				}); err != nil {
+					t.Fatal(err)
+				}
+			})
+
+			msg := message.New(log.New(os.Stderr, "clean: ", 0))
+			msg.SwapVerbose(testing.Verbose())
+			c, err := pkg.Open(t.Context(), msg, 0, 0, 0, base)
+			if err != nil {
+				t.Fatal(err)
+			}
+			t.Cleanup(c.Close)
+
+			all := pkg.Collect(slices.Concat(tc.a, tc.keep))
+			if _, _, err = c.Cure(&all); !pkg.IsCollected(err) {
+				t.Fatal(err)
+			}
+
+			var (
+				idents    []unique.Handle[pkg.ID]
+				checksums []unique.Handle[pkg.Checksum]
+			)
+			idents, checksums, err = c.Clean(false, tc.inputs, tc.keep...)
+			if err != nil {
+				t.Fatalf("Clean: error = %v", err)
+			}
+			var buf [2]pkg.Checksum
+
+			slices.SortFunc(idents, func(a, b unique.Handle[pkg.ID]) int {
+				buf[0], buf[1] = a.Value(), b.Value()
+				return bytes.Compare(buf[0][:], buf[1][:])
+			})
+			slices.SortFunc(checksums, func(a, b unique.Handle[pkg.Checksum]) int {
+				buf[0], buf[1] = a.Value(), b.Value()
+				return bytes.Compare(buf[0][:], buf[1][:])
+			})
+
+			if !slices.Equal(idents, tc.wantIdents) {
+				t.Errorf(
+					"Clean: idents = %s, want %s",
+					formatHandles(idents...), formatHandles(tc.wantIdents...),
+				)
+			}
+			if !slices.Equal(checksums, tc.wantChecksums) {
+				t.Errorf(
+					"Clean: checksums = %s, want %s",
+					formatHandles(checksums...), formatHandles(tc.wantChecksums...),
+				)
+			}
+
+			want := tc.want.hash()
+			var checksum pkg.Checksum
+			if err = pkg.HashDir(&checksum, base); err != nil {
+				t.Fatalf("HashDir: error = %v", err)
+			} else if checksum != want {
+				t.Error(expectsFrom(base.String()))
+			}
+		})
+	}
+}
diff --git a/internal/pkg/pkg.go b/internal/pkg/pkg.go
index 883798a4..262ff667 100644
--- a/internal/pkg/pkg.go
+++ b/internal/pkg/pkg.go
@@ -816,6 +816,28 @@ func (e *ChecksumMismatchError) Error() string {
 		" instead of " + Encode(e.Want)
 }
 
+// LinknamePrefixError describes a malformed linkname to a [Checksum].
+type LinknamePrefixError string
+
+func (e LinknamePrefixError) Error() string {
+	return "linkname " + strconv.Quote(string(e)) + " missing prefix"
+}
+
+// readlinkChecksum reads a symbolic link to a dirChecksum entry and saves the
+// decoded [Checksum] to the value pointed to by buf. The checksumLinknamePrefix
+// is required.
+func readlinkChecksum(a *check.Absolute, buf *Checksum) error {
+	linkname, err := os.Readlink(a.String())
+	if err != nil {
+		return nil
+	}
+
+	if !strings.HasPrefix(linkname, checksumLinknamePrefix) {
+		return LinknamePrefixError(linkname)
+	}
+	return Decode(buf, linkname[len(checksumLinknamePrefix):])
+}
+
 // ScrubError describes the outcome of a [Cache.Scrub] call where errors were
 // found and removed from the underlying storage of [Cache].
 type ScrubError struct {
diff --git a/internal/pkg/pkg_test.go b/internal/pkg/pkg_test.go
index d5c92a6d..a4fb8361 100644
--- a/internal/pkg/pkg_test.go
+++ b/internal/pkg/pkg_test.go
@@ -486,7 +486,17 @@ func checkWithCache(t *testing.T, testCases []cacheTestCase) {
 					tc.early(t, base)
 				}
 				tc.f(t, base, c)
-				scrubFunc = func() error { return c.Scrub(1 << 7) }
+				scrubFunc = func() error {
+					err = c.Scrub(1 << 7)
+					idents, checksums, cleanErr := c.Clean(false, false)
+					if len(idents) > 0 {
+						t.Errorf("destroyed %d idents", len(idents))
+					}
+					if len(checksums) > 0 {
+						t.Errorf("destroyed %d checksums", len(checksums))
+					}
+					return errors.Join(err, cleanErr)
+				}
 			}
 
 			var restoreTemp bool
@@ -561,10 +571,7 @@ func checkWithCache(t *testing.T, testCases []cacheTestCase) {
 			if err := pkg.HashDir(&checksum, base); err != nil {
 				t.Fatalf("HashDir: error = %v", err)
 			} else if checksum != want {
-				t.Fatalf("(scrubbed) HashDir: %v", &pkg.ChecksumMismatchError{
-					Got:  checksum,
-					Want: want,
-				})
+				t.Fatalf("(scrubbed) %s", expectsFrom(base.String()))
 			}
 		})
 	}